Fig. 5: THUMPD2 and LARP7 independently and interdependently affect alternative splicing.
RNAs from HCT116 WT and THUMPD2 KO cells treated with a non-target siRNA or one targeting LARP7 (LARP7 KD) were subjected to mRNA-seq (n = 3 independent experiments) and alternative splicing analysis was performed. a, b UpSet plots showing the number of alternative splicing events detected as significant in the indicated comparisons with respect to wild-type (WT) or between LARP7 KD (L7 KD) and THUMPD2 KO (TD2 KO). a Significant AS events quantified with rMATS (FDR < 0.01, absolute inclusion difference > 0.1, median read count in at least one condition > 50). b Significant IR events based on splicing efficiency calculation of annotated introns (p value < 0.01, absolute inclusion difference > 0.05, median read count in at least one condition > 50). c IR event specifically regulated by THUMPD2. d A3SS event specifically regulated by LARP7. e Skipped exon event with more exon skipping in any condition than WT. f Distribution of significant and not significant inclusion differences for different AS types and conditions. Statistical analysis was performed using the two-sided Wilcoxon rank-sum test and Bonferroni correction. Box limits (hinges) represent the 25th to 75th percentiles (Interquartile Range (IQR)), lines indicate medians, whiskers extend from the hinge to the minima and maxima that are not further than 1.5x IQR from the hinge, and outliers are represented as dots. g Correlations between inclusion level differences between THUMPD2 KO (left) / LARP7 KD (right) respective to WT to inclusion level differences resulting from the combination of THUMPD2 KO & LARP7 KD in cells. Error band represents the 95% confidence interval (CI) for the fitted linear regression line. h, i Inclusion level differences resulting from the combination of THUMPD2 KO & LARP7 KD in cells is better explained by a weighted combination of the individual lack of either THUMPD2 or LARP7 in cells. A scaling factor of 0.6 (dashed line in (i)) improves the overall correlation the most. i Correlations between inclusion level differences resulting from the combined THUMPD2 KO & LARP7 KD. Error band represents the 95% confidence interval (CI) for the fitted linear regression line.
